bims-ginsta 2026-04-05 papers

bims-ginsta

Biomed News

on Genome instability

Issue of 2026–04–05
33 papers selected by
Jinrong Hu, National University of Singapore

Specialized high-capacity mitochondria fuel cell invasion.
DNA damage burden causes selective CUX2 neuron loss in neuroinflammation.
Actomyosin contractility drives apical polarization and membrane transport during tubulogenesis.
Mechanosensory channels mediate ER Ca2+ transients to trigger assembly of autophagosome initiation sites for degradation of ER subdomains.
Gene regulatory landscape dissected by single-cell four-omics sequencing.
Cellular and spatial remodeling of aging breast tissue revealed.
MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy.
Perturb-seq uncovers pathological obstacles to direct cardiac reprogramming in vivo.
Compartmentalized cytoplasmic tradewinds direct soluble proteins.
Mosaic gastruloids reveal a temporal restriction for developmental cell competition.
Single-cell spatial atlas of the aging human breast.
Developmental organization of sensory and sympathetic ganglia.
Programmable macromolecule delivery via engineered trogocytosis.
A convergent uPAR-positive tumor ecosystem creates broad vulnerability to CAR T cell therapy.
Genome-wide DNA supercoiling arises from transcription and SMC activity and mediates transcriptional negative feedback.
Multiomic single-cell perturbation screens reveal critical lncRNA regulators of senescence.
Spindle pole proteins confine chromosomes to ensure their expulsion during female meiosis.
Expansion of outer cortical CUX2 neurons requires adaptations for DNA repair.
U2AF regulates the translation and localization of nuclear-encoded mitochondrial mRNAs.
Structure of the mouse cytoplasmic lattice.
Dynamics and consequences of differential RNA isoform production during cardiomyocyte fate determination and early-stage maturation.
Mad1 facilitates α5 integrin trafficking from the Golgi to promote abscission during cytokinesis.
Retinol saturase in the mitochondria antagonizes IDH2 and GLUD1 acetylation to mediate heart repair.
Distinct mechanisms of replication stress induced by oncogenic RAS and cyclin E1 converge on R-loop-dependent fork reversal.
Unveiling the molecular architecture of T cells and immune synapses with cryo-expansion microscopy.
Hippo signaling differentially regulates distal progenitor subpopulations and their transitional states to construct the mammalian lungs.
A Novel Eukaryotic Ribosome Factor Enables Translation Restart Following Cellular Dormancy.
Mitochondrial remodeling in skeletal muscle underlies exercise-induced reversal of age-associated functional decline in mice and humans.
2'-O-Methylation maintains ribosome structural and translation integrity.
Condensate protein aggregation in ALS/FTD is regulated by GGGGCC-repeat RNA scaffolds.
Endometrial epithelial cells with high ALDH activity control uterine development and regeneration.
Versatile SMAD2 and SMAD3 epitope-tagged mouse models for genomic profiling of TGFβ signaling: Uncovering GDF9-SMAD2/3 targets.
Lipid turnover and GEF recruitment collectively determine Rab5 recruitment and activation during the first step of early endosome formation.

Curr Biol. 2026 Apr 01. pii: S0960-9822(26)00310-6. [Epub ahead of print]

Specialized high-capacity mitochondria fuel cell invasion.

Isabel W Kenny-Ganzert, Lena P Basta, Lianzijun Wang, Qiuyi Chi, Laura C Kelley, Caitlin Y Su, Jake Leyhr, Katherine S Morton, Joel N Meyer, David R Sherwood.

  Cell invasion through basement membrane (BM) is energetically intensive. How cells produce high ATP levels to power invasion is understudied. By endogenously tagging 20 mitochondrial proteins, we identified a specialized mitochondrial subpopulation within the C. elegans anchor cell (AC) that localizes to the BM breaching site and generates elevated ATP levels to fuel invasion. These electron transport chain (ETC)-enriched high-capacity mitochondria are compositionally unique, harboring increased protein import machinery and dense cristae enriched with ETC components. High-capacity mitochondria emerge at the time of AC specification and depend on the AC pro-invasive transcriptional program. Finally, we show that netrin signaling through an Src kinase directs microtubule polarization, facilitating metaxin adaptor complex-dependent ETC-enriched mitochondrial trafficking to the AC invasive front. Our studies reveal that an invasive cell produces high ATP levels by generating and localizing high-capacity mitochondria. This might be a common strategy used by other cells to meet the energetically demanding processes.

Keywords:  ATP; basement membrane; cell invasion; cell specification; electron transport chain; live imaging; mitochondria; mitochondrial dynamics

DOI:  https://doi.org/10.1016/j.cub.2026.03.023
Nature. 2026 Apr 01.

DNA damage burden causes selective CUX2 neuron loss in neuroinflammation.

Laura Morcom, Wenlong Xia, Zhaoyang Xu, Yashika Awasthi, Celine Geywitz, Matthew O Ellis, Tomas Noli, Amel Zulji, Daniel Yamamoto, Gemma C Girdler, Li Kai, Keying Zhu, Mingming Wei, Xiao-Yan Tang, Kimberly K Hoi, Julio Gonzalez-Maya, Greg J Duncan, Adrien M Vaquie, Diana Gold Diaz, Riki Kawaguchi, Erdong Liu, Yu Sun, Denny Yang, Gregory D Jordan, I-Ling Lu, Staffan Holmqvist, Theresa Bartels, Katherine Ridley, Jennifer Ja-Yoon Choi, Santos J Franco, Eric J Huang, Ben Emery, Daniel Geschwind, Lucas Schirmer, Gabriel Balmus, Brian Popko, Stephen P J Fancy, David H Rowitch.

Neurodegeneration shows regional and cell-type-specific patterns in ageing and disease1, but the underlying mechanisms for cell-type-specific neuronal losses remain poorly understood. Previous studies have shown that upper cortical layer thinning occurs in progressive human multiple sclerosis (MS) and that cortical layer 2 and layer 3 (L2/3) excitatory neurons (L2/3ENs) that express CUT-like homeobox 2 (CUX2) are selectively vulnerable to degeneration2. Here we report that L2/3ENs within MS cortical lesions have an elevated DNA damage burden. DNA damage and selective loss of L2/3ENs were recapitulated in diverse mouse models of demyelination and pan-cortical inflammation, confirming their intrinsic vulnerability. Functions of Cux2 and activating transcription factor 4 (Atf4) were essential for resilience of L2/3ENs during postnatal neuroinflammation, acting in neurons to enhance DNA double-strand break repair. Interferon-γ, a cytokine implicated in MS pathogenesis3,4, was sufficient to elevate levels of reactive oxygen species, leading to DNA damage-mediated neuronal death in vitro, and caused selective depletion of L2/3 neurons in mice. These findings indicate that DNA damage burden and inadequate repair in CUX2+ L2/3ENs contributes to selective vulnerability in neuroinflammatory injury.

DOI: https://doi.org/10.1038/s41586-026-10310-3
Res Sq. 2026 Mar 25. pii: rs.3.rs-7665826. [Epub ahead of print]

Actomyosin contractility drives apical polarization and membrane transport during tubulogenesis.

Yuji Mizotani, Edwin Munro.

Lumen formation during tubulogenesis requires the large-scale redistribution of cellular material, but the in vivo mechanisms remain unclear. Using the ascidian notochord as a tractable model, we show that actomyosin contractility orchestrates sequential, spatially distinct modes of cortical and cytoplasmic transport to promote lumen initiation and growth: lateral actomyosin centralizes apical determinants on cell contacts to position apical lumens; cyclic detachment and inward contraction of actomyosin bundles from a basal equatorial contractile ring drives internalization and transport of basal membranes toward the apical lumen surface to enable lumen growth. Basal membrane internalization/transport and lumen growth require both Ezrin/Radixin/Moesin (ERM) proteins and extracellular matrix (ECM). ERM promotes equatorial contractility and transmits inward contractile forces to basal membranes, while broad attachment to ECM resists inward forces to promote equatorial detachment. These findings reveal how cells integrate cortical and cytoplasmic modes of transport, driven by actomyosin contractility, to enable rapid lumen formation and likely other types of cellular remodeling.

DOI: https://doi.org/10.21203/rs.3.rs-7665826/v1
Mol Cell. 2026 Apr 02. pii: S1097-2765(26)00158-9. [Epub ahead of print]86(7): 1377-1396.e6

Mechanosensory channels mediate ER Ca2+ transients to trigger assembly of autophagosome initiation sites for degradation of ER subdomains.

Xiaoli Ma, Zhiyang Cheng, Hongyu Zhao, Huan Zhang, Ke Xiao, Jiali Xie, Yun Feng, Chun Yang, Yujie Feng, Xi Wang, Yaozu Xiang, Junjie Hu, Qiaoxia Zheng, Wei Ji, Hong Zhang.

  ER-phagy involves the selective autophagosomal engulfment of ER fragments, but the signaling events, selection mechanisms, and membrane source of ER-phagic autophagosomes remain elusive. Here, using state-of-the-art super-resolution multi-SIM imaging, we reveal that stresses (prolonged starvation, cholesterol dyshomeostasis, and high-Ca2+ insults) trigger the expansion of sheet ER subdomains containing high levels of luminal Ca2+ in mammalian cells, which are subsequently degraded by ER-phagy. Autophagosome formation and sequestration of ER sheets require the concerted actions of FAM134B and lipidated LC3, whereas the autophagy proteins ATG14 and ATG9 are partially dispensable. Electron microscopy and cryo-electron tomography show that the membranes of autophagosomes enclosing high-Ca2+-containing ER sheets are directly remodeled from the ER. The ER-localized cation channels PIEZO1 and TRPV1 are enriched at and mediate Ca2+ transients from high-Ca2+-containing ER sheets, triggering liquid-liquid phase separation of the autophagosome-initiating FIP200 complex to initiate ER-phagy. Thus, distinct mechanisms are employed for the formation of high-Ca2+-containing ER-enclosing autophagosomes and non-selective autophagosomes.

Keywords:  Ca(2+); ER-phagy; FAM134B; FIP200; PIEZO1; TRPV1

DOI:  https://doi.org/10.1016/j.molcel.2026.03.002
Nature. 2026 Apr 01.

Gene regulatory landscape dissected by single-cell four-omics sequencing.

Yujie Chen, Zhiyuan Liu, Heming Xu, Jiayu Liu, Mengxuan Wang, Yi Chi, Boyuan Liang, Menghan Liu, Yongli Peng, Hao Ge, Dong Xing.

Cellular diversity is governed not only by the transcriptome but also by multiple layers of epigenomic regulation, including nucleosome occupancy, chromatin states and genome architecture1-3. Here, to comprehensively understand how these regulatory modalities converge to shape cellular identity, we developed a single-cell four-omics sequencing method that enables parallel profiling of genome conformation, histone modifications, chromatin accessibility and gene expression within the same cell (CHARM). Applying CHARM to mouse embryonic stem cells and cortical tissues, we reconstructed integrated epigenome profiles, uncovering distinct cell-cycle dynamics of chromatin accessibility and histone modification, and spatial clustering of regulatory elements in three-dimensional nuclear space. Leveraging an interpretable machine learning model, we further identified thousands of enhancer-promoter linkages with high accuracy that modulate gene expression in a cell-type- and subtype-specific manner. Together, CHARM enables integrative dissection of the three-dimensional epigenome at single-cell resolution, providing a versatile platform for decoding the regulatory landscape across diverse cells in complex tissues.

DOI: https://doi.org/10.1038/s41586-026-10322-z
Nat Aging. 2026 Mar 31.

Cellular and spatial remodeling of aging breast tissue revealed.

DOI: https://doi.org/10.1038/s43587-026-01111-4
Nat Struct Mol Biol. 2026 Apr 01.

MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy.

Stephen P Burr, Kathryn Auckland, Angelos Glynos, Abhilesh Dhawanjewar, Cameron Ryall, Wei Wei, Antony Hynes-Allen, Malwina Prater, Matylda Sczaniecka-Clift, Julien Prudent, Patrick F Chinnery, Jelle van den Ameele.

Mitochondria contain their own genome, mitochondrial DNA (mtDNA), which is under strict control by the cell nucleus. mtDNA occurs in many copies per cell and mutations often only affect a proportion of them, giving rise to heteroplasmy. mtDNA copy number and heteroplasmy level together shape the tissue-specific impact of mtDNA mutations, eventually giving rise to both rare mitochondrial and common neurodegenerative diseases. Here, we use MitoPerturb-Seq for CRISPR-Cas9-based, high-throughput single-cell interrogation of the nuclear genes and pathways that sense and control mtDNA copy number and heteroplasmy. We screened a panel of mtDNA maintenance genes in mouse cells with a heteroplasmic mtDNA mt-Ta mutation. This revealed both common and perturbation-specific aspects of the integrated stress response to mtDNA depletion caused by Tfam, Opa1 and Polg knockout. These responses are only partially mediated by ATF4 and cause cell-cycle stage-independent slowing of cell proliferation. MitoPerturb-Seq, thus, provides experimental insight into disease-relevant mitochondrial-nuclear interactions and may inform development of therapies targeting cell-type- and tissue-specific vulnerabilities to mitochondrial dysfunction.

DOI: https://doi.org/10.1038/s41594-026-01779-7
Cell Stem Cell. 2026 Mar 30. pii: S1934-5909(26)00116-5. [Epub ahead of print]

Perturb-seq uncovers pathological obstacles to direct cardiac reprogramming in vivo.

Yihong Cai, Yang Yang, Junbo Yang, Ruohan Ding, Qihan Zhang, Xin Dang, Chenxuan Li, Yang Zhao.

  Direct induction of cardiomyocytes from fibroblasts represents a promising strategy for cardiac regeneration. However, the transdifferentiation efficiency in vivo remains low. Leveraging a Perturb-seq platform tailored to complex pathological environments, we systematically compared and ranked 140 potential barriers of in vivo cardiac reprogramming. Based on their shRNA distribution and enrichment along the single-cell RNA-seq trajectory, calreticulin (Calr) emerged as a top inhibitor. Calr knockdown greatly enhanced iCM induction efficiency in vitro, enabling synchronized calcium oscillations in iCMs, and accelerated in situ reprogramming after myocardial infarction, improving cardiac function and reducing fibrosis. Mechanistically, Calr knockdown activates calcium signaling, boosting MEF2C activity to drive reprogramming and even substitute for exogenous MEF2C. Collectively, our study reveals critical regulators hindering in situ cardiomyocyte induction in a pathological microenvironment, providing effective reprogramming factors and a strategic framework for cardiac repair and regeneration after myocardial infarction.

Keywords:  Calr; Perturb-seq; calcium signaling; calreticulin; cardiac fibrosis; cardiac reprogramming; heart repair; in vivo reprogramming; myocardal infarction; regenerative medicine

DOI:  https://doi.org/10.1016/j.stem.2026.03.006
Nat Commun. 2026 Mar 30. pii: 2589. [Epub ahead of print]17(1):

Compartmentalized cytoplasmic tradewinds direct soluble proteins.

Catherine G Galbraith, Brian P English, Ulrike Boehm, James A Galbraith.

Proteins essential for signaling, morphogenesis, and migration traverse the complex intracellular landscape via vesicular trafficking, microtubule-based transport, and diffusion. However, the precise mechanisms guiding soluble proteins toward their functional destinations have remained elusive. Here, we demonstrate that soluble proteins are directed toward the cell's advancing edge through advection-diffusion enhanced by intracellular fluid flow. We reveal that advective transport occurs within a specialized compartment at the cell's leading edge, separated from the rest of the cytoplasm by an actin-myosin condensate barrier. The barrier limits protein mixing between the compartment and the rest of the cytoplasm, maintaining localized protein concentrations. Contraction at the barrier generates a molecularly non-specific fluid flow that drives the forward movement of treadmilling actin monomers, actin-binding proteins, adhesion molecules, and even inert proteins. Dynamic changes in the local curvature of the barrier steer the fluid flow to direct proteins toward protrusive regions of the leading edge. This advective mechanism synchronizes protein distribution with local changes in cell morphology. Outside this compartment, diffusion dominates as the principal mode of soluble protein transport. Our findings uncover previously unrecognized compartmentalization strategies that regulate soluble protein concentrations and coordinate their efficient distribution for homeostasis, protrusion, and adhesion.

DOI: https://doi.org/10.1038/s41467-026-70688-6
Nat Cell Biol. 2026 Apr 01.

Mosaic gastruloids reveal a temporal restriction for developmental cell competition.

Joshua D Frenster, Stephen Babin, Pablo Casani-Galdon, Joel B Josende-Garcia, Pau Pascual-Mas, Gaëlle Robertson, Shlomit Edri, Alexandra E Wehmeyer, Sebastian J Arnold, Jordi Garcia Ojalvo, Alfonso Martinez Arias.

Selective elimination of suboptimal cells is critical for the developmental integrity of early mammalian embryogenesis. Cell competition is a non-autonomous quality control in which 'winner' cells outcompete viable but suboptimal 'loser' cells based on fitness differences. Here we investigate cell competition dynamics using mosaic mouse gastruloids, a 3D embryonic stem cell-based model of gastrulation. Introducing just two Trp53-deficient supercompetitor cells suffices to impair growth in neighbouring wild-type cells through mitochondrial apoptosis. Competition is tightly restricted to a developmental transition stage between primed pluripotency and early gastrulation and involves gene regulatory networks of pluripotency exit. Heterochronic gastruloids from developmental stage-shifted cells, EpiGastruloids, and dynamic p53-degrons reveal that both winners and losers must reside within this permissive stage, during which acute relative p53 protein levels determine competitive outcomes. These findings advance our understanding of cell fitness evaluation and establish gastruloids as a powerful 3D model for investigating developmental stage-specific cell competition in mammalian embryogenesis.

DOI: https://doi.org/10.1038/s41556-026-01923-x
Nat Aging. 2026 Mar 31.

Single-cell spatial atlas of the aging human breast.

Pulkit Gupta, Eric Lee, Neus Masqué Soler, Ellen Schrader, Xiao Qian Wang, Shimrit Mayer, Cristina Flores, Sean Beatty, Andrew Roth, Samuel Aparicio, H Raza Ali.

Breast cancer can develop over a wide age range and tumors in younger women differ from those in older women. Aging alters the spatial context of early tumors and may explain these differences, but breast tissue aging remains poorly characterized. Here, using imaging mass cytometry to profile the spatial expression of 40 proteins, we explore age-related remodeling of normal breast tissues in over 3 million cells from 527 reduction mammoplasties. Aged breast tissue was less cellular and less proliferative for all cell types (epithelial, stromal and immune). Tissue architecture was restructured with fewer heterotypic epithelial cell-cell interactions, far fewer lobules and increased fat. Older tissues had a more inflammatory microenvironment with increased M2 macrophages and granzyme B+ T cells, contrasted by younger tissues in which B cells were most enriched. Our multiscale atlas extensively details an unexpected general decline of breast tissue with age and reveals its changing spatial context.

DOI: https://doi.org/10.1038/s43587-026-01104-3
Nature. 2026 Apr 01.

Developmental organization of sensory and sympathetic ganglia.

Keng Ioi Vong, Yanina D Alvarez, Qingquan Zhang, Jiaming Weng, Geoffroy Noel, Scott T Barton, Changuk Chung, Robyn Howarth, Naomi Meave, Fiza Jiwani, Sai B Patarlapalli, Fenyong Yao, Fugui Zhu, Chelsea Barrows, Arzoo Patel, Jian Xiong Wang, Neil C Chi, Stephen F Kingsmore, Melanie D White, Xiaoxu Yang, Joseph G Gleeson.

The neural crest generates a broad spectrum of cell types that migrate across the body plan to populate multiple tissues1. However, the relationship between lineages of neural crest derivatives remains unclear, and the extent to which neural crest cells delaminated from the neural tube have specified fates remains debated. Here, leveraging CRISPR barcoding in mice and mosaic variant barcode analysis in humans, we demonstrate robust bilateral progenitor clonal spread of neural crest progenitors along the rostrocaudal axis but limited clonal overlap between sensory and sympathetic lineages. Computational modelling of mosaic variants suggests that most neural crest cells show strong fate restriction before delamination. Real-time imaging of quail embryos further shows a fibroblast-growth-factor-dependent rostrocaudal dispersion of neural crest cells across multiple axial levels. These findings support a model in which neural crest fate bias predominantly emerges within the neural tube, with only a minor subset of delaminated progenitors retaining multipotency to generate both sensory and sympathetic derivatives.

DOI: https://doi.org/10.1038/s41586-026-10313-0
Nat Cell Biol. 2026 Apr 01.

Programmable macromolecule delivery via engineered trogocytosis.

Xinyi Chen, Yinglin Situ, Yuexuan Yang, Luna Lyu, Mengting Han, Lorenzo Magni, Maylin L Fu, Boxiong Deng, Sui Wang, Lei S Qi.

Trogocytosis, the transfer of plasma membrane fragments during cell-cell contact, offers potential for macromolecular delivery but is limited by the uncertain fate of trogocytosed molecules, restriction to membrane cargo and unclear generalizability. Here we demonstrate that donor cells engineered with designed receptors specific to surface ligands can transfer proteins to recipient cells through direct contact. We identified key engineering principles for enhancing transfer and ensuring cargo functionalization, including receptor design, pH-responsive membrane fusion, inducible cargo localization and release, and subcellular translocation. The method is broadly applicable across diverse cell types and operates through a dynamin- and endosome acidification-dependent pathway. Exploiting these findings, we developed TRANSFER, a versatile delivery system with programmable cell type specificity and tunability. TRANSFER can sense multiple ligand inputs, deliver large therapeutic protein cargos and mediate genome editing. The study establishes trogocytosis as a programmable, versatile framework for cell-based macromolecular delivery.

DOI: https://doi.org/10.1038/s41556-026-01920-0
Cell. 2026 Mar 30. pii: S0092-8674(26)00269-2. [Epub ahead of print]

A convergent uPAR-positive tumor ecosystem creates broad vulnerability to CAR T cell therapy.

Zeda Zhang, Yu-Jui Ho, Xin Fang, Minseo Kim, Marguerite Li, Wei Luan, Clemens Hinterleitner, Sascha Haubner, Friederike Kogel, Edwin C Pratt, Elif Ozcelik, José Reyes, Qingwen Jiang, Vincent W Yang, Yu-Jung Chen, Tao Wang, Haijiao Liu, Haonan Hu, Xueqian Zhuang, Jin Park, Stella V Paffenholz, Kevin Chen, Qing Chang, Amanda Kulick, Jing Zhang, Eric Chan, Eric Rosiek, Ning Fan, Riley A Williams, Adam C Wang, Samuel Freeman, Sha Tian, Gertrude Gunset, Andreina Garcia Angus, Nicolas Lecomte, Selma Yeni Yildirim, Emily Ali, Michelle Wu, Ileana C Miranda, Cristina R Antonescu, Olca Basturk, Zeynep Tarcan, Natasha Rekhtman, Christina Wilson, Merve Basar, Jennifer L Sauter, Hikmat A Al-Ahmadie, Samuel Singer, Christine Iacobuzio-Donahue, Charles Rudin, Elisa de Stanchina, Karuna Ganesh, Paul B Romesser, Britta Weigelt, Dan Dongeun Huh, Josef Leibold, Judith Feucht, Ignacio Vázquez-García, Matthew J Bott, Dmitriy Zamarin, Sohrab P Shah, Jason S Lewis, Corina Amor, Dana Pe'er, Jorge Mansilla-Soto, Aveline Filliol, Michel Sadelain, Scott W Lowe.

  Chimeric antigen receptor (CAR) T cells have transformed hematologic cancer therapy but remain limited in solid tumors by antigen heterogeneity and a suppressive, pro-fibrotic microenvironment. We previously identified the urokinase plasminogen activator receptor (uPAR) as upregulated in senescent, pro-fibrotic cells and showed that uPAR-directed CAR T cells could safely reverse fibrosis in mice. Integrative analyses now reveal that uPAR is broadly expressed in solid tumors enriched for TP53 and RAS pathway mutations. These tumors adopt a progenitor-like state supported by a niche of uPAR-positive stromal cells with senescence features. Human uPAR CAR T cells eliminate tumor cells and their stromal support, induce durable regressions across diverse models, eradicate systemic metastases, and are potentiated by senescence-inducing therapies. Importantly, these cells achieve robust antitumor activity without sustained myelosuppression in mice reconstituted with human immune systems. Together, these findings establish uPAR as a broadly applicable CAR T target capable of overcoming major barriers in solid tumor therapy.

Keywords:  CAR T cells; fibrosis; p53; senescence; senolytic; tumor microenvironment; uPAR

DOI:  https://doi.org/10.1016/j.cell.2026.03.002
bioRxiv. 2026 Mar 26. pii: 2026.03.26.714539. [Epub ahead of print]

Genome-wide DNA supercoiling arises from transcription and SMC activity and mediates transcriptional negative feedback.

Linying Zhu, Qian Yao, Charan Vemuri, Chongyi Chen.

Genome-wide DNA supercoiling is closely linked to chromatin organization and gene expression, yet the mechanisms establishing genome-scale supercoiling in living cells and its functional consequences remain unclear. Here, we show that genome-wide supercoiling arises from transcription-driven asymmetric topological relaxation together with contributions from SMC complexes in human cells. During RNA polymerase elongation, human topoisomerases preferentially relax positive over negative supercoils, leading to the accumulation of negative supercoiling around genes. This imbalance enriches supercoiling at transcriptionally active regions including TAD boundaries, and promotes the emergence of large-scale topology. In parallel, SMC complexes independently shape genome-wide supercoiling, with cohesin contributing to interphase topology and condensin establishing an overall positively supercoiled mitotic genome. Functionally, the accumulation of transcription-driven negative supercoiling represses local transcription, revealing a supercoiling-mediated negative feedback mechanism. Together, these findings define the mechanistic basis of genome-scale supercoiling in human cells and establish DNA topology as an integral regulatory layer of transcription.

DOI: https://doi.org/10.64898/2026.03.26.714539
Nat Aging. 2026 Mar 31.

Multiomic single-cell perturbation screens reveal critical lncRNA regulators of senescence.

Shouxuan Zhu, Sunyang Ying, Donghong Cai, Ya Ren, Luoxi Wang, Zhi Qi, Vera Gorbunova, Jing-Dong J Han.

Long noncoding RNAs (lncRNAs) regulate transcriptional and epigenetic programs during aging and senescence. However, no comprehensive studies have systematically integrated multilayered analyses to reveal their diverse regulatory roles. Moreover, lncRNAs with therapeutic potential in age-related diseases remain unexplored. Here we systematically perturbed 32 high-abundance aging- and senescence-associated lncRNAs (PtbAlncs) using a Perturb-seq-based CRISPR-dCas9-KRAB knockdown system coupled with single-nucleus multiomics profiling, enabling simultaneous transcriptomic and chromatin accessibility analysis. This analysis uncovered essential roles for previously uncharacterized lncRNAs in senescence regulation, validated computationally and experimentally. These lncRNAs modulate distinct single-cell RNA-sequencing modules through diverse yet overlapping epigenetic motifs in single-cell ATAC-sequencing modules. Among them, HOTAIRM1, a DNA repair-associated PtbAlnc, stabilizes DNA repair by cooperating with BANF1 and p53 at double-strand break loci within condensates. Its deficiency impairs DNA repair and triggers p53-mediated senescence. In aged mouse lungs, adeno-associated virus-mediated HOTAIRM1 overexpression reduced fibrosis, alleviated tissue damage, and promoted cellular proliferation, underscoring its therapeutic potential.

DOI: https://doi.org/10.1038/s43587-026-01100-7
bioRxiv. 2026 Mar 25. pii: 2026.03.24.713942. [Epub ahead of print]

Spindle pole proteins confine chromosomes to ensure their expulsion during female meiosis.

Kan Yaguchi, Lifeng Chen, Abdollah Mohammadi-Sangcheshmeh, Judith Tafur, Nicole E Familiari, Edward J Grow, Michael K Rosen, Jeffrey B Woodruff.

Animal oocytes undergo highly asymmetric divisions to expel excess copies of their genome into compact cells called polar bodies. This requires tight clustering and cortical positioning of meiotic chromosomes, yet the mechanism remains incompletely understood. Using C. elegans oocytes, we found that the meiotic spindle pole protein ZYG-9/ch-TOG delocalizes from microtubules to spread along the surface of chromosomes and prevent their dispersal in meiotic anaphase. This effect was more pronounced in the absence of the spindle, where ZYG-9 formed into a micron-scale droplet that enveloped all chromosomes. Purified ZYG-9 was sufficient to bind DNA and coat reconstituted chromatin. Mutations that perturb ZYG-9-DNA binding impaired chromosome packaging into polar bodies, resulting in oocytes carrying extra chromosomes and reduced fertility. We propose that liquid-like assemblies of spindle pole proteins are repurposed as surface-acting glue to tightly package meiotic chromosomes into polar bodies, thus ensuring oocytes have the correct genome copy number.

DOI: https://doi.org/10.64898/2026.03.24.713942
Nature. 2026 Apr 01.

Expansion of outer cortical CUX2 neurons requires adaptations for DNA repair.

Wenlong Xia, Laura Morcom, Zhaoyang Xu, I-Ling Lu, Qing Wang, Kimberly K Hoi, Mingming Wei, Keying Zhu, Gregory Jordan, Xiao-Yan Tang, Julio Gonzalez-Maya, Vanesa S Mattera, Sophia M Panigrahi, Riki Kawaguchi, Ben Emery, Santos J Franco, Daniel H Geschwind, Brian Popko, David H Rowitch, Stephen P J Fancy.

During mammalian evolution, excitatory neurons in upper cortical layer 2 and layer 3 (L2/3) have shown a disproportionate expansion compared with other layers1-4. Replicative expansion of cortical neural progenitors is associated with considerable oxidative DNA damage. Here we show that activating transcription factor 4 (ATF4) has roles as a critical regulator of the DNA damage response, directly activating components of double-stranded DNA repair, including CIRBP, UBA52 and EBF1. Notably, pan-cortical knockout (Emx1-Cre;Atf4fl/fl) demonstrates that ATF4 is required specifically for the development of upper layer 2/3 neurons, marked by the expression of cut-like homeobox 2 protein, CUX2. ATF4 functions to repair DNA damage and attenuate cell death of embryonic radial glial progenitors in a p53-dependent manner. In particular, we show that cold inducible RNA-binding protein (CIRBP) is a transcriptional target of ATF4 that is required for normal phosphorylation of the key double-strand DNA repair factor ataxia telangiectasia mutated (ATM). These findings establish that ATF4 is an essential regulator of the DNA damage response. They further indicate that there are extraordinary requirements for DNA repair after replicative stress in CUX2+ neurons during mammalian brain development.

DOI: https://doi.org/10.1038/s41586-026-10290-4
Mol Cell. 2026 Apr 02. pii: S1097-2765(26)00162-0. [Epub ahead of print]86(7): 1293-1310.e14

U2AF regulates the translation and localization of nuclear-encoded mitochondrial mRNAs.

Gloria R Garcia, Murali Palangat, Josquin Moraly, Benjamin T Donovan, Bixuan Wang, Ira Phadke, David Sturgill, Jiji Chen, Guofeng Zhang, Ronald J Holewinski, Brittney Short, Gustavo A Rivero, David M Swoboda, Naomi Taylor, Kathy McGraw, Daniel R Larson.

  The mechanisms underlying molecular targeting to mitochondria remain enigmatic, yet this process is crucial for normal cellular function. The RNA-binding proteins U2AF1 and U2AF2 form a heterodimer (U2AF) that shuttles between the nucleus and cytoplasm, regulating splicing in the nucleus and translation in the cytoplasm. Our study in human bronchial epithelial cells (HBECs) identifies an unexpected role for U2AF in mitochondrial function. We demonstrate that U2AF interacts with nuclear-encoded mitochondrial (NE-mt) mRNAs and proteins, inhibits translation, localizes to the mitochondria, and regulates mRNA localization to mitochondria. Moreover, an oncogenic point mutation in U2AF1(S34F) disrupts this regulation, leading to altered mitochondrial structure, increased translation, large changes in the mitochondria proteome, and oxidative phosphorylation (OXPHOS)-dependent metabolic rewiring, recapitulating changes observed in bone marrow progenitors from patients with myelodysplastic syndromes. These findings reveal a non-canonical role for U2AF, where it modulates multiple aspects of mitochondrial function by regulating the translation and mitochondrial localization of nuclear-encoded mRNAs.

Keywords:  U2AF1; cancer; mRNA localization; metabolism; mitochondria; myeloid leukemia; translation

DOI:  https://doi.org/10.1016/j.molcel.2026.03.006
Nature. 2026 Mar 31.

Structure of the mouse cytoplasmic lattice.

Pengliang Chi, Xiang Wang, Jialu Li, Jingrui Huang, Sicheng Ju, Sibei Liu, Li Yan, Yuechao Lu, Zihan Zhang, Zhuo Han, Jinhong Li, Qianqian Qi, Qingting Liu, Yiren Zeng, Li Guo, Xiaofeng Zhang, Long Gui, Dong Deng.

The fertilized egg relies almost entirely on maternal stores in the oocyte to ensure the successful initiation of development1. The cytoplasmic lattices (CPLs) in mammalian oocytes store maternal-expressed proteins and play an essential role in embryogenesis2,3. Impairing multiple CPL members leads to early embryonic arrest (EEA), resulting in infertility in mammals. However, the mechanism underlying the assembly and storage of CPLs remains largely unknown. Here, we report the cryo-EM structure of a native mouse CPL repeating unit (~ 4 MDa) at 3.74 Å resolution. This repeating unit exhibits a tripartite architecture comprising a framework, extended linkers, and a CPL core. The external framework is built from PADI6 decamers and the subcortical maternal complexes (SCMC). Two linkers formed by NLRP4F polymerize the frameworks into an extended filament. In CPL core, the epigenetic regulator UHRF1 is trapped by PADI6, UBE2D, and NLRP14 in a compact, autoinhibited conformation that prevents nuclear entry and ubiquitin ligase activity. Moreover, the CPL core stores GTP-bound α/β-tubulin heterodimers and inactive SCF E3-ubiquitin ligase components (FBXW-SKP1 complex) in a poised but restrained state. These features establish CPLs as a dynamic regulatory pool that enables rapid microtubule assembly and tightly controlled ubiquitination during the oocyte-to-embryo transition. Together, this semi-in-situ structure illuminates CPL assembly and storage-module organization, and establishes CPLs as specialized proteostasis organelles for maternal regulation in oocytes and early embryonic development.

DOI: https://doi.org/10.1038/s41586-026-10442-6
Genome Res. 2026 Apr 03. pii: gr.281150.125. [Epub ahead of print]

Dynamics and consequences of differential RNA isoform production during cardiomyocyte fate determination and early-stage maturation.

Joanna Delimata-Raczek, Natalia Koralewska, Bart Krist, Magdalena Rakoczy, Marek Figlerowicz, Ireneusz Stolarek.

Cellular identity is dictated by precise transcriptomic programs, however, the mechanisms that dynamically shape the transcriptome by producing diverse RNA isoforms remain incompletely understood. Here, through longitudinal transcriptomic profiling of cardiomyogenesis, we delineate pervasive RNA isoform switching across the developmental trajectory of cardiac differentiation. We show that the changes in isoform accumulation are largely decoupled from shifts in overall gene expression levels and arise predominantly from alternative transcription start and termination rather than splicing. This regulatory layer preferentially targets genes essential for cardiac function, specifically those encoding contractile machinery and ion channel complexes. We demonstrate that genes undergoing isoform switching without changing overall expression constitute a functionally distinct cohort, establishing isoform switching as an independent layer of gene regulation. Furthermore, we characterize stage-specific expression dynamics for numerous RNA-binding proteins and link their expression to specific isoform switching events. Our findings support a coordinated mechanism for the targeted regulation of RNA diversity, positioning isoform switching as a primary driver of transcriptomic maturation during lineage commitment.

DOI: https://doi.org/10.1101/gr.281150.125
Nat Commun. 2026 Mar 30.

Mad1 facilitates α5 integrin trafficking from the Golgi to promote abscission during cytokinesis.

Daniel K Sam, Greta Grems, Anjon Audhya, Beth A Weaver.

Mad1 is an essential component of the mitotic spindle assembly checkpoint. During interphase, Mad1 regulates the trafficking of α5 integrin from the Golgi to the plasma membrane. Here, we show that depletion of Mad1 or α5 integrin induces cytokinesis failure. Though the cytokinetic furrow ingresses with normal timing, it ultimately regresses, resulting in cytokinesis failure. We identify an ~300 amino acid internal fragment of Mad1 that is necessary and sufficient for the Golgi localization of Mad1. This fragment, which we term Mad1-Golgi, can rescue α5 integrin secretion and cytokinesis in Mad1-depleted cells. Expression of exogenous α5 integrin is sufficient to overcome the cytokinesis defect caused by Mad1 depletion. The contribution of both Mad1 and α5 integrin to cytokinesis is observed specifically under adherent growth conditions, and a pool of both proteins localizes to the midbody in adherent cells. These results demonstrate a previously uncharacterized role for Mad1 in cytokinesis by regulating α5 integrin secretion from the Golgi apparatus.

DOI: https://doi.org/10.1038/s41467-026-70928-9
Proc Natl Acad Sci U S A. 2026 Apr 07. 123(14): e2526203123

Retinol saturase in the mitochondria antagonizes IDH2 and GLUD1 acetylation to mediate heart repair.

Wenya Ma, Yanan Tian, Jianglong Li, Qimeng Ouyang, Lei Xu, Bowei Zhang, Hongyang Chen, Hanjing Li, Yuqing Lin, Yu Hu, Zhongyu Ren, Yifu Shen, Xin Wang, Xinlu Gao, Xiuxiu Wang, Yining Liu, Ye Tian, Yu Liu, Zhenwei Pan, Benzhi Cai.

  Facilitating endogenous cardiomyocyte proliferation has emerged as an important strategy for cardiac repair. Conserved retinol saturase (Retsat) functions in producing all-trans 13,14-dihydroretinol in the endoplasmic reticulum (ER). However, Retsat's role and mechanism in heart regeneration remain unclear. Here, we uncover that Retsat is upregulated in cardiomyocytes during cardiac regeneration in mice. Cardiomyocyte-specific Retsat knockin promotes cardiac regeneration and improves cardiac function after injury. Conversely, cardiomyocyte-specific knockout of Retsat inhibits heart regeneration in neonatal mice. Surprisingly, Retsat drives cardiomyocyte proliferation independently of its classical retinol saturase activity in the ER. Retsat also localizes in cardiomyocyte mitochondria, and mitochondrial-specific overexpression of Retsat can stimulate cardiomyocyte proliferation and heart repair after injury. Mechanistically, Retsat in the mitochondria acts as an antagonist of Idh2 and Glud1 acetylation, reducing their acetylation levels and enhancing their activities. Furthermore, Retsat enters mitochondria by interacting with Tom70 and Tim23 proteins. These data suggest that targeting Retsat is a promising strategy for promoting cardiac regeneration after heart injury.

Keywords:  Glud1; Idh2; Retsat; cardiomyocyte proliferation

DOI:  https://doi.org/10.1073/pnas.2526203123
Nat Commun. 2026 Apr 03.

Distinct mechanisms of replication stress induced by oncogenic RAS and cyclin E1 converge on R-loop-dependent fork reversal.

Anna Oravetzova, Marketa Dvorakova, Anca-Irina Mihai, Martin Andrs, Margarita Sobol, Anton Zuev, Kaustubh Shukla, Barbora Boleslavska, Vinicio Rosano, Christiane König, Jiri Prokes, Hana Hanzlikova, Libor Macurek, Jana Dobrovolna, Pavel Janscak.

Activated oncogenes elicit genomic instability by inducing DNA replication stress. Here we show that replication fork reversal and chromosome mis-segregation induced by oncogenic RAS (HRASV12) or cyclin E1 overexpression are largely caused by co-transcriptional RNA:DNA hybrids (R-loops) formed during S-phase. Furthermore, we demonstrate that replication stress induced by HRASV12, but not cyclin E1, is driven by reactive oxygen species (ROS) in a manner dependent on the replisome-associated ROS sensor peroxiredoxin 2 (PRDX2) and is linked to PRDX2-mediated release of the fork acceleration factor TIMELESS from the replisome. Inhibition of fork reversal in cells overexpressing HRASV12 or cyclin E1 induces unrestrained DNA synthesis mediated by the MUS81 endonuclease and the primase-polymerase PRIMPOL, thereby promoting proper chromosome segregation in mitosis. These results establish PRIMPOL repriming as part of the MUS81-dependent replication restart mechanism that operates at sites of R-loop-mediated transcription-replication conflicts to maintain genomic stability. Furthermore, our data indicate that, despite their protective role during S-phase, persistent reversed forks impair chromosome segregation in mitosis, potentially leading to DNA breaks and chromosomal rearrangements.

DOI: https://doi.org/10.1038/s41467-026-71353-8
Cell Rep. 2026 Apr 01. pii: S2211-1247(26)00243-3. [Epub ahead of print]45(4): 117165

Unveiling the molecular architecture of T cells and immune synapses with cryo-expansion microscopy.

Florent Lemaître, Olivier Mercey, Isabelle Mean, Elise Paulin, Valérie Dutoit, Jan A Rath, Christine von Gunten, Denis Migliorini, Caroline Arber, Paul Guichard, Virginie Hamel, Benita Wolf.

  Cytotoxic T cell killing is executed at the immunological synapse, whose nanoscale organization underlies function but remains difficult to resolve in native states. Here, we apply cryo-expansion microscopy (cryo-ExM) to visualize the near-native three-dimensional architecture of human T cell synapses and cytotoxic organelles. Cryo-ExM preserves actin, microtubules, membranes, and fine membrane protrusions with high fidelity, enabling volumetric quantification of synapse morphogenesis. We identify an adhesion-dependent, dome-like membrane architecture beneath activated T cells that collapses upon ICAM-1 engagement, linking synapse topology to adhesive cues. Cryo-ExM further resolves intact lytic granules in primary human CD4 and CD8 T cells, revealing single-core and multi-core ultrastructures, spatial organization, and perforin and granzyme loading. Using tissue-adapted expansion microscopy, we map cytotoxic granule content in tumor-infiltrating T cells in FFPE human brain tumors. Together, these data establish a near-native structural framework for human T cell cytotoxicity and an imaging workflow bridging cell models and clinical tissues.

Keywords:  3D ultrastructure; CP: immunology; T cell cytotoxicity; cryo-expansion microscopy; cytotoxic granule deployment; immune synapse; lytic granules; tumor-infiltrating lymphocytes

DOI:  https://doi.org/10.1016/j.celrep.2026.117165
Nat Commun. 2026 Apr 03.

Hippo signaling differentially regulates distal progenitor subpopulations and their transitional states to construct the mammalian lungs.

Kuan Zhang, Madhuri Basak, Youssef Zaher, Erica Yao, Shao-An Wang, Thin Aung, Pao-Tien Chuang.

Lung size control and cell type specification are key unresolved issues. In this study, we have engineered mosaic patterns of Hippo signaling to reveal the developmental potential of SOX9+ progenitors at the distal lung buds. Our results show that the distal SOX9+ subdomain is sufficient to direct lung outgrowth through bifurcation, providing a mechanism for lung size control. Through single-cell analyses, we identify transitional cell states and candidates for promoting cell fates. Moreover, genetic analysis reveals that Hippo signaling induces distinct cell fates at different SOX9+ subdomains to produce the conducting airways and the alveolar epithelium. These results provide the first extensive map of the developmental paths of lung cells. Some of the developmental paths of transitional cell states in mice correspond to those in human lungs. Together, these studies provide mechanistic insight into how Hippo signaling controls the sequential expansion and differentiation of SOX9+ progenitors to construct the mammalian lungs.

DOI: https://doi.org/10.1038/s41467-026-71253-x
bioRxiv. 2026 Mar 24. pii: 2026.03.21.713407. [Epub ahead of print]

A Novel Eukaryotic Ribosome Factor Enables Translation Restart Following Cellular Dormancy.

Maciej Gluc, Higor Rosa, Maria Bozko, Lesley A Turner, Cassidy R Prince, Yelena Peskova, Heather A Feaga, Kathleen L Gould, Simone Mattei, Ahmad Jomaa.

Dormancy is a survival strategy employed by all domains of life to withstand prolonged nutrient deprivation and environmental stress that is marked by a global shutdown of protein synthesis. However, the molecular mechanisms driving ribosome inactivation and reactivation during and after dormancy in eukaryotes remain poorly understood. Here, we identify SNOR, a novel SBDS-like ribosome-associated factor in Schizosaccharomyces pombe, that is upregulated and associates with ribosomes during induced dormancy triggered by glucose depletion. SNOR contributes to protein synthesis repression by binding the ribosome to probe the peptidyl transferase center (PTC), block tRNA-binding sites, and cap the polypeptide exit tunnel (PET). Importantly, we show that SNOR is essential for the restart of protein synthesis upon glucose reintroduction and exit from dormancy. SNOR is evolutionarily conserved and specifically upregulated in response to glucose stress in fungi. These findings reveal a previously unrecognized ribosome-associated factor that links glucose stress and cellular dormancy to surveillance of protein synthesis and highlight the power of in situ structural biology to uncover stress-responsive regulators of translation.

DOI: https://doi.org/10.64898/2026.03.21.713407
Proc Natl Acad Sci U S A. 2026 Apr 07. 123(14): e2508286123

Mitochondrial remodeling in skeletal muscle underlies exercise-induced reversal of age-associated functional decline in mice and humans.

Esther García-Domínguez, Cristina García-Domínguez, José Luis Cabrera-Alarcón, María Del Mar Muñoz-Hernández, Pablo Hernansanz-Agustín, Andrea Curtabbi, Julio Domenech-Fernandez, Enrique Calvo, Jesús Vázquez, Antonio L Serrano, Pura Muñoz-Cánoves, Gloria Olaso-González, José Antonio Enríquez, María Carmen Gómez-Cabrera.

  Loss of skeletal muscle mass and strength are common manifestations of frailty in older people and are linked to reduced quality of life. However, whether mitochondria are mechanistically linked to frailty and how physical activity, or lack thereof, is involved in age-related functional decline are still unknown. We report that exercise-induced improvements in functional capacity, including reduced frailty in old mice, are dependent on mitochondrial adaptations in skeletal muscle at structural, enzymatic, and functional levels. Our preclinical study included a healthy aging mouse line, a transgenic model of robustness, and a muscle-specific mitochondrial-deficient mutant mice, allowing us to assess both mitochondrial plasticity with aging and the necessity of intact mitochondrial function for exercise-induced adaptations. These findings were corroborated by a cross-sectional human study examining the relationship between skeletal muscle mitochondrial function, age, and physical capacity. We analyzed biopsies from 30 donors (men and women, aged 17 to 99 y) stratified into young and older adults with varying functional statuses. Our results indicate that mitochondrial dysfunction in skeletal muscle is associated with the decline in locomotor muscle function in the elderly, highlighting the potential role of exercise or habitual physical activity in mitigating this phenotype. Notably, we demonstrate that skeletal muscle mitochondria maintain plasticity during aging in mice and humans, and that this preserved adaptability can be leveraged to improve muscle performance and overall functional capacity.

Keywords:  frailty; health span; mitochondrial function; proteomics; sarcopenia

DOI:  https://doi.org/10.1073/pnas.2508286123
Mol Cell. 2026 Apr 01. pii: S1097-2765(26)00164-4. [Epub ahead of print]

2'-O-Methylation maintains ribosome structural and translation integrity.

Yu Zhao, Jay Rai, Lauren N Cohen, Yuerong Shu, Chong Xu, Hemant Goswami, Xin Chen, Hong Jin, Virginie Marchand, Yuri Motorin, Homa Ghalei, Hong Li.

  In eukaryotic ribosomes, ∼2% of RNA nucleotides undergo 2'-O-methylation, a conserved cellular mechanism thought to be critical for maintaining and regulating translation. Here, we use ribosome profiling, translation assays, proteomics, and high-resolution structural analyses to show that loss of native 2'-O-methylation in yeast ribosomes disproportionally affects the translation of ribosomal protein transcripts, driven by changes in codon usage and recognition of structured RNA. Translation reprogramming by the hypomethylated ribosomes is supported by reduced thermostability and high-resolution evidence of altered ribosomal structures and conformations. Consistent with the roles of the affected proteins in sustaining cellular fitness, hypomethylated ribosomes under stress exhibit a selective loss of downregulated proteins and misassembly associated with methylation loss. Our data provide structural and mechanistic insights into how 2'-O-methylation supports ribosome integrity and mediates cellular stress responses.

Keywords:  IRES translation; RNA 2′-O-methylation; Ribo-seq; box C/D snoRNPs; fibrillarin; ribosome stability; translation; translation fidelity

DOI:  https://doi.org/10.1016/j.molcel.2026.03.008
Nat Struct Mol Biol. 2026 Mar 31.

Condensate protein aggregation in ALS/FTD is regulated by GGGGCC-repeat RNA scaffolds.

Yu Liu, Minghui Song, Liqi Wan, Pei Guo, Da Han.

Biomolecular condensates regulate essential biological processes relevant to health and disease. However, the mechanisms driving pathogenic condensate formation and their therapeutic targeting have not been fully elucidated. In amyotrophic lateral sclerosis and frontotemporal dementia caused by C9orf72 GGGGCC repeat expansions (c9ALS/FTD), the expanded repeat RNA and repeat-associated non-AUG translation products are key pathogenic factors. Here, we show that the GGGGCC-repeat RNA and poly(GR) form cocondensates in vitro and in cellulo. The G-quadruplex and hairpin structures of GGGGCC-repeat RNA act as scaffolds to accelerate liquid-to-solid phase transition and aggregation of poly(GR), with the hairpin structure promoting amorphous solid-like condensates in vitro and reducing poly(GR) mobility. The cocondensation of GGGGCC-repeat RNA and poly(GR) exacerbates nucleolar stress and cellular toxicity. Targeting both G-quadruplex and hairpin structures of GGGGCC-repeat RNA with small molecules diminishes poly(GR) aggregation and ameliorates cellular dysfunction. These findings expand our understanding of poly(GR) aggregation in c9ALS/FTD, highlight the importance of RNA structure in regulating protein aggregation and suggest that targeting the RNA scaffold may expand the druggable space of pathogenic condensates.

DOI: https://doi.org/10.1038/s41594-026-01785-9
Res Sq. 2026 Mar 24. pii: rs.3.rs-6831916. [Epub ahead of print]

Endometrial epithelial cells with high ALDH activity control uterine development and regeneration.

Diana Monsivais, Suni Tang, Anna Unser, Peixin Jiang, Sydney Parks, Genesis Herrera, Ting Geng, Linda Alpuing-Radilla, Brooke Thigpen, Xiaoming Guan.

Adult stem cells are thought to drive the regenerative potential of the endometrium and contribute to the pathogenesis of endometriosis, however, their identity and defining features remain to be characterized. Here, we used in vivo and in vitro approaches to demonstrate that cells with high aldehyde dehydrogenase 1 activity (ALDH HI cells) were long lived progenitors in the endometrial epithelium with a higher organoid formation capacity, long-term passaging potential, and stemness gene signatures. Using lineage tracing with an Aldh1a1 cre/ERT2 ; ROSA26 tdTomato reporter mouse, Aldh1a1 + cells expanded during postnatal development, estrus cycling, and following post-partum repair. In response to ovariectomy or exogenous estradiol, we found that ALDH1A1 + cells localized to glandular crypts of the endometrium or throughout the luminal epithelium, respectively, indicating that their spatial localization is hormone sensitive. Functionally, we found that selective ablation of ALDH1A1 + cells in Aldh1a1 cre/ERT2 ; ROSA26- DTR flox/flox mice decreased endometrial gland number and FOXA2 expression . These findings were recapitulated in the human endometrium, where endometrial epithelial organoids with high ALDH activity (ALDH HI cells) showed a higher organoid formation capacity than ALDH LO cells and displayed unique transcriptomes with fewer luminal-like ciliated cells. Overall, our studies indicate that ALDH1A1 + cells are hormone-sensitive adult stem cells in the endometrium with regenerative potential that are critical for endometrial development and function.

DOI: https://doi.org/10.21203/rs.3.rs-6831916/v2
Proc Natl Acad Sci U S A. 2026 Apr 07. 123(14): e2600071123

Versatile SMAD2 and SMAD3 epitope-tagged mouse models for genomic profiling of TGFβ signaling: Uncovering GDF9-SMAD2/3 targets.

Zian Liao, Qian Zhang, Keisuke Shimada, Kaori Nozawa, Suni Tang, Masahito Ikawa, Diana Monsivais, Martin M Matzuk.

  Transforming growth factor β (TGFβ) signaling pathways are integral for a plethora of biological processes. SMAD2 and SMAD3 are the principal transcriptional effectors of TGFβ superfamily ligands, yet quantitative, genome-wide mapping of their DNA-associated complexes under physiological contexts has remained limited due to the lack of specific, robust models. Here, we generated two versatile epitope-tagged mouse models in which endogenous SMAD2 and SMAD3 proteins are globally tagged with hemagglutinin (HA) and podoplanin (PA) sequences, respectively, enabling high-fidelity profiling of SMAD2 and SMAD3 binding across tissues. To demonstrate the broad application of our models, we exemplified the usage of our lines in ovarian biology, where we defined the transcriptional programs downstream of GDF9, a key oocyte-derived ligand in folliculogenesis from the TGFβ superfamily. By integrating genomic and transcriptomic analyses, we identified direct genes induced by the GDF9-SMAD2/3 axis and identified gene sets suppressed by this signaling cascade, highlighting a previously underappreciated role of GDF9 in attenuating competing pathways to ensure proper ovarian granulosa cell fate transitions. Short-term GDF9 stimulation shifts SMAD2/3 cofactor recruitment toward lineage- and differentiation-associated transcription factors, without significant global changes in H3K27ac landscapes, indicating that GDF9 signals through targeted SMAD recruitment to preacetylated chromatin regions. Network analyses further demonstrated that GDF9-SMAD2/3 direct targets align with luteinizing hormone-driven preovulatory signaling. Together, our study generated epitope-tagged mouse models that provide extensive and applicable in vivo genetic toolkits for tissue-specific dissection of TGFβ family signaling and reveal a comprehensive, direct transcriptional network through which GDF9 coordinates granulosa cell differentiation and follicular maturation.

Keywords:  GDF9; SMADs; TGFβ; granulosa cells; oocyte secreted factors

DOI:  https://doi.org/10.1073/pnas.2600071123
Nat Commun. 2026 Mar 30.

Lipid turnover and GEF recruitment collectively determine Rab5 recruitment and activation during the first step of early endosome formation.

Yongtao Du, Xilin Miao, Yu Gao, Yu Liang, Xue Bai, Song Dang, Zhongsheng Wu, Zhengyang An, Xinyi Zhang, Yaran Yang, Zhe Zhang, Huaqing Cai, Kangmin He.

Early endosomes are the pivotal sorting station in eukaryotic cells. A longstanding critical question is how the small GTPase Rab5 is precisely targeted to the correct membrane to initiate early endosome formation. Here, we identify Rabex5 and hRME6 as the two guanine-nucleotide exchange factors (GEFs) that together regulate Rab5 recruitment during early endosome formation. Single-molecule imaging of genome-edited cells reveals that Rabex5 and hRME6 are recruited continuously or transiently to nascent uncoated endocytic carriers, respectively. However, in contrast to uncoated endocytic carriers and other intracellular organelles, directing Rabex5 or its GEF domain to clathrin-coated pits or the plasma membrane fails to trigger Rab5 recruitment. Both in vivo and in vitro experiments show that the plasma membrane-enriched phospholipid PI(4,5)P2 prevents Rab5 association with the plasma membrane. Importantly, we found that impaired hydrolysis of PI(4,5)P2 led to reduced early endosome formation in Lowe syndrome cells. Therefore, the spatiotemporal recruitment and activation of Rab5 during early endosome formation are collectively determined by Rabex5/hRME6 recruitment and PI(4,5)P2 depletion during uncoated endocytic carrier formation.

DOI: https://doi.org/10.1038/s41467-026-70543-8